Now I get your question. The SEO redirect is applied to both web sites, while the HTTP->HTTPS redirect is obviously only applied to the HTTP web site. So I guess it cannot be done in ISPConfig, not even by adding an Apache Directive (which would get applied to both websites again), without modifying server/conf/vhost.conf.master

True @Jesse Norell , I first thought applying it to both sites would create a loop, but as we check for ^domain\.tld$ first, it works.
So @A.Bauer you can also add the following two lines to your apache directives and disable both redirects in ISPConfig:
RewriteCond %{HTTP_HOST} ^domain\.tld$ [NC]
RewriteRule ^(.*)$ https://www.domain.tld$1 [R=301,NE,L]